Job ID = 7116777 SRX = SRX8639485 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:17:29 prefetch.2.10.7: 1) Downloading 'SRR12117049'... 2020-07-22T06:17:29 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:19:47 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:19:47 prefetch.2.10.7: 1) 'SRR12117049' was downloaded successfully 2020-07-22T06:19:47 prefetch.2.10.7: 'SRR12117049' has 0 unresolved dependencies Read 21879518 spots for SRR12117049/SRR12117049.sra Written 21879518 spots for SRR12117049/SRR12117049.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:34 21879518 reads; of these: 21879518 (100.00%) were paired; of these: 11907609 (54.42%) aligned concordantly 0 times 9152351 (41.83%) aligned concordantly exactly 1 time 819558 (3.75%) aligned concordantly >1 times ---- 11907609 pairs aligned concordantly 0 times; of these: 141341 (1.19%) aligned discordantly 1 time ---- 11766268 pairs aligned 0 times concordantly or discordantly; of these: 23532536 mates make up the pairs; of these: 23319126 (99.09%) aligned 0 times 168402 (0.72%) aligned exactly 1 time 45008 (0.19%) aligned >1 times 46.71% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 94709 / 10090983 = 0.0094 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:33:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Jul 2020 15:33:44: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:33:44: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:33:50: 1000000 INFO @ Wed, 22 Jul 2020 15:33:56: 2000000 INFO @ Wed, 22 Jul 2020 15:34:03: 3000000 INFO @ Wed, 22 Jul 2020 15:34:09: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Jul 2020 15:34:14: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:34:14: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:34:16: 5000000 INFO @ Wed, 22 Jul 2020 15:34:21: 1000000 INFO @ Wed, 22 Jul 2020 15:34:23: 6000000 INFO @ Wed, 22 Jul 2020 15:34:27: 2000000 INFO @ Wed, 22 Jul 2020 15:34:30: 7000000 INFO @ Wed, 22 Jul 2020 15:34:34: 3000000 INFO @ Wed, 22 Jul 2020 15:34:37: 8000000 INFO @ Wed, 22 Jul 2020 15:34:41: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Jul 2020 15:34:44: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:34:44: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:34:44: 9000000 INFO @ Wed, 22 Jul 2020 15:34:48: 5000000 INFO @ Wed, 22 Jul 2020 15:34:51: 1000000 INFO @ Wed, 22 Jul 2020 15:34:51: 10000000 INFO @ Wed, 22 Jul 2020 15:34:55: 6000000 INFO @ Wed, 22 Jul 2020 15:34:58: 2000000 INFO @ Wed, 22 Jul 2020 15:34:58: 11000000 INFO @ Wed, 22 Jul 2020 15:35:02: 7000000 INFO @ Wed, 22 Jul 2020 15:35:05: 3000000 INFO @ Wed, 22 Jul 2020 15:35:06: 12000000 INFO @ Wed, 22 Jul 2020 15:35:10: 8000000 INFO @ Wed, 22 Jul 2020 15:35:12: 4000000 INFO @ Wed, 22 Jul 2020 15:35:13: 13000000 INFO @ Wed, 22 Jul 2020 15:35:17: 9000000 INFO @ Wed, 22 Jul 2020 15:35:19: 5000000 INFO @ Wed, 22 Jul 2020 15:35:21: 14000000 INFO @ Wed, 22 Jul 2020 15:35:24: 10000000 INFO @ Wed, 22 Jul 2020 15:35:26: 6000000 INFO @ Wed, 22 Jul 2020 15:35:28: 15000000 INFO @ Wed, 22 Jul 2020 15:35:31: 11000000 INFO @ Wed, 22 Jul 2020 15:35:33: 7000000 INFO @ Wed, 22 Jul 2020 15:35:36: 16000000 INFO @ Wed, 22 Jul 2020 15:35:38: 12000000 INFO @ Wed, 22 Jul 2020 15:35:41: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:35:44: 17000000 INFO @ Wed, 22 Jul 2020 15:35:45: 13000000 INFO @ Wed, 22 Jul 2020 15:35:48: 9000000 INFO @ Wed, 22 Jul 2020 15:35:51: 18000000 INFO @ Wed, 22 Jul 2020 15:35:52: 14000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:35:55: 10000000 INFO @ Wed, 22 Jul 2020 15:35:59: 19000000 INFO @ Wed, 22 Jul 2020 15:35:59: 15000000 INFO @ Wed, 22 Jul 2020 15:36:02: 11000000 INFO @ Wed, 22 Jul 2020 15:36:07: 16000000 INFO @ Wed, 22 Jul 2020 15:36:07: 20000000 INFO @ Wed, 22 Jul 2020 15:36:08: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:36:08: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:36:08: #1 total tags in treatment: 9877506 INFO @ Wed, 22 Jul 2020 15:36:08: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:36:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:36:09: #1 tags after filtering in treatment: 7135917 INFO @ Wed, 22 Jul 2020 15:36:09: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Jul 2020 15:36:09: #1 finished! INFO @ Wed, 22 Jul 2020 15:36:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:36:09: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:36:09: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Jul 2020 15:36:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:36:10: 12000000 INFO @ Wed, 22 Jul 2020 15:36:14: 17000000 INFO @ Wed, 22 Jul 2020 15:36:17: 13000000 INFO @ Wed, 22 Jul 2020 15:36:21: 18000000 INFO @ Wed, 22 Jul 2020 15:36:24: 14000000 INFO @ Wed, 22 Jul 2020 15:36:28: 19000000 INFO @ Wed, 22 Jul 2020 15:36:31: 15000000 INFO @ Wed, 22 Jul 2020 15:36:35: 20000000 INFO @ Wed, 22 Jul 2020 15:36:36: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:36:36: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:36:36: #1 total tags in treatment: 9877506 INFO @ Wed, 22 Jul 2020 15:36:36: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:36:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:36:37: #1 tags after filtering in treatment: 7135917 INFO @ Wed, 22 Jul 2020 15:36:37: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Jul 2020 15:36:37: #1 finished! INFO @ Wed, 22 Jul 2020 15:36:37: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:36:37: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:36:37: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Jul 2020 15:36:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:36:38: 16000000 INFO @ Wed, 22 Jul 2020 15:36:45: 17000000 INFO @ Wed, 22 Jul 2020 15:36:51: 18000000 INFO @ Wed, 22 Jul 2020 15:36:58: 19000000 INFO @ Wed, 22 Jul 2020 15:37:04: 20000000 INFO @ Wed, 22 Jul 2020 15:37:06: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:37:06: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:37:06: #1 total tags in treatment: 9877506 INFO @ Wed, 22 Jul 2020 15:37:06: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:37:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:37:06: #1 tags after filtering in treatment: 7135917 INFO @ Wed, 22 Jul 2020 15:37:06: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Jul 2020 15:37:06: #1 finished! INFO @ Wed, 22 Jul 2020 15:37:06: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:37:06: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:37:06: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Jul 2020 15:37:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639485/SRX8639485.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling